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SYY_STAAE_1_420

Tyrosine--tRNA ligase [Class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily]

Composition of the binding site

Protein chains monomer
A1 (SYY_STAAE):36:40, 42, 45, 46, 49, 50, 53, 54, 70, 75, 80, 103, 124, 170, 174, 177, 190, 192, 193, 195, 196, 19936:40, 42, 45, 46, 49, 50, 53, 54, 70, 75, 80, 103, 124, 170, 174, 177, 190, 192, 193, 195, 196, 199

Full PDB list

1jii, 1jij, 1jik, 1jil

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
3
6
C
3
7
G
3
8
A
3
9
D
4
0
L
4
6
H
5
0
P
5
3
F
5
4
L
7
0
T
7
5
D
8
0
I
1
0
3
N
1
2
4
Y
1
7
0
Q
1
7
4
D
1
7
7
Q
1
9
0
G
1
9
2
G
1
9
3
D
1
9
5
Q
1
9
6
[1]1jii.a 38329 . . . . . . . . . . . . . . . . . . . . . .
[1]1jij.a 62929 . . . . . . . . . . . . . . . . . . . . . .
[1]1jik.a 54533 . . . . . . . . . . . . . . . . . . . . . .
[1]1jil.a 48527 . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
Y
3
6
C
3
7
G
3
8
A
3
9
D
4
0
T
4
2
S
4
5
L
4
6
G
4
9
H
5
0
P
5
3
F
5
4
L
7
0
T
7
5
D
8
0
I
1
0
3
N
1
2
4
Y
1
7
0
Q
1
7
4
D
1
7
7
Q
1
9
0
G
1
9
2
G
1
9
3
D
1
9
5
Q
1
9
6
N
1
9
9
[1]1jii.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jij.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jik.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jil.a . . . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1jii.a:383
1jij.a:629
1jik.a:545
1jil.a:485
[1] 1jii.a
0.6
0.8 0.9 0.7
[1] 1jij.a 0.4
0.4
0.8 0.7
[1] 1jik.a 0.8 0.5
0.2
0.4
[1] 1jil.a 1.1 0.9 1.4
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1jii.a
1jij.a
1jik.a
1jil.a
[1] 1jii.a
0
.03 .07 .07
[1] 1jij.a .03
0
.06 .06
[1] 1jik.a .07 .06
0
.07
[1] 1jil.a .07 .06 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1jii.a
1jij.a
1jik.a
1jil.a
[1] 1jii.a
0
0.3 0.6 0.5
[1] 1jij.a 0.3
0
0.5 0.5
[1] 1jik.a 0.6 0.5
0
0.4
[1] 1jil.a 0.5 0.5 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1jii.a
1jij.a
1jik.a
1jil.a
[1] 1jii.a
0
0.5 1.0 0.9
[1] 1jij.a 0.5
0
0.9 0.9
[1] 1jik.a 1.0 0.9
0
0.7
[1] 1jil.a 0.9 0.9 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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